I did some tests and suspect that mining ZEN, ZEC or ZCL might be the problem. Winminer is mining them normally and reports earnings, but... eventually they do not show up in the graph, nor do they register in my account!
So, does ZEN or ZEC mining require a long stable mining time to register coins in Winminer? That might explain the issue.

I have disabled these coins and wait to see the results...

EDIT: I've contacted Winminer help again and they solved the issue. Moreover they registered the "lost" mining effort in my account! Many thanks to them for all their help.